rs1386389

Variant names:

• chr4-111032114-A-C
• rs1386389
• ENST00000681682.1:n.494-85036A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-111032114-A-C
• chr4-111032114-A-G
• chr4-111032114-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681682.1(ENSG00000288692):​n.494-85036A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,226 control chromosomes in the GnomAD database, including 7,592 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7592 hom., cov: 31)
• Consequence: ENSG00000288692 ENST00000681682.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288692	ENST00000681682.1	n.494-85036A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46678 AN: 151106 Hom.: 7565 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.297

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 46752 AN: 151226 Hom.: 7592 Cov.: 31 AF XY: 0.308 AC XY: 22745 AN XY: 73860

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.304

Alfa AF: 0.265 Hom.: 7311

Bravo AF: 0.321

Asia WGS AF: 0.382 AC: 1324 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1386389; hg19: chr4-111953270;